Hi,<br>I simulated one crystallize protein (from pdb) having amino acid entry from 24 to 740. 1 to 23 residues was missing.<br><br>When i am plotting RMSF for each residues by following command<br>g_rmsf -f md.tpr -s md.trr (with the help of Grace)<br>
<br>I am getting plot from 1 to 717 residues. I Think in prior step of simulation, gromacs changed the residues number of original pdb file and allotted the new number, that why residue 24 now become residue 1. <br><br>
I want to analyze RMSF at the spacific residue 340 from pdb entry but after simulation it become 317. Their is no problem in analysing RMSF value at 317 but actual problem in potting it is comming 340. <br><br>My question is that How i can plot RMSF from residue number 24 to 740, Which is actually in PDB file. <br>
<br>Regards<br>Rituraj<br><br><br><br><br><br><div class="gmail_quote">On Tue, Dec 15, 2009 at 4:30 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. freeze backbone & Pressure scaling error ( ??? )<br>
2. typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS)<br>
(Pradip Biswas)<br>
3. Re: typo in ffoplsaanb.itp for opls_179 (OS) and opls_180<br>
(OS) (Mark Abraham)<br>
4. Re: Freeze backbone & Pressure scaling more than 1%<br>
(Mark Abraham)<br>
5. Hi (ashish pandey)<br>
6. Re: Hi (XAvier Periole)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 15 Dec 2009 13:56:44 +0900 (KST)<br>
From: " ??? " <<a href="mailto:chemgirl@hanmail.net">chemgirl@hanmail.net</a>><br>
Subject: [gmx-users] freeze backbone & Pressure scaling error<br>
To: "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 14 Dec 2009 23:00:30 -0600<br>
From: Pradip Biswas <<a href="http://biswas.pk" target="_blank">biswas.pk</a>@<a href="http://gmail.com" target="_blank">gmail.com</a>><br>
Subject: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and<br>
opls_180 (OS)<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:2301c61d0912142100g675259cfxd374d9adaacff093@mail.gmail.com">2301c61d0912142100g675259cfxd374d9adaacff093@mail.gmail.com</a>><br>
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<br>
Hi,<br>
<br>
The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are<br>
typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM,<br>
these oxygen atoms are being recognized as Nitrogen atoms.<br>
<br>
Biswas.<br>
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<br>
Message: 3<br>
Date: Tue, 15 Dec 2009 16:33:28 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and<br>
opls_180 (OS)<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4B271FA8.2030309@anu.edu.au">4B271FA8.2030309@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Pradip Biswas wrote:<br>
> Hi,<br>
><br>
> The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are<br>
> typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing<br>
> QMMM, these oxygen atoms are being recognized as Nitrogen atoms.<br>
<br>
DvdS fixed this in the git source earlier this week.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 15 Dec 2009 16:36:10 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Freeze backbone & Pressure scaling more than<br>
1%<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4B27204A.3030602@anu.edu.au">4B27204A.3030602@anu.edu.au</a>><br>
Content-Type: text/plain; charset=EUC-KR<br>
<br>
이진희 wrote:<br>
><br>
><br>
> Dear all<br>
><br>
><br>
><br>
> When I run produnction run using freeze backbone in GROMACS 4.0.5, the<br>
> error was shown.<br>
><br>
> But I didn't use freeze backboone, the error wasn't shown.<br>
><br>
> ------------------------------------------------<br>
><br>
> Step 1 Warning: Pressure scaling more than 1%.<br>
><br>
> ------------------------------------------------<br>
><br>
> I changed "tau_p" value from 0.5 to 5 in md.mdp file, but the above<br>
> error was shown.<br>
><br>
> I don't know how to solve it. Any one give some advice.<br>
<br>
Provide a full description. What's the system, how big is it, how did<br>
you equilibrate it, why/how are you freezing the backbone, does the run<br>
finish, does the trajectory look ok?<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 15 Dec 2009 14:22:39 +0530<br>
From: ashish pandey <<a href="mailto:ashishpandey12@gmail.com">ashishpandey12@gmail.com</a>><br>
Subject: [gmx-users] Hi<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:f2be40f50912150052l6f04594ct5817933f4bae8e4a@mail.gmail.com">f2be40f50912150052l6f04594ct5817933f4bae8e4a@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Dear all,<br>
my self ashish and i am trying to dynamics using gromacs.<br>
i am new in these field. in the time of running Pdb2gmx to create .gro<br>
file. i am geting these error.<br>
<br>
Fatal error:<br>
Atom HA in residue MET 1 not found in rtp entry with 9 atoms<br>
<br>
please help me sortout these problem.<br>
<br>
--<br>
Ashish Pandey<br>
NIPER India<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Tue, 15 Dec 2009 10:03:29 +0100<br>
From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>
Subject: Re: [gmx-users] Hi<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:F925B208-9BF1-4C79-AC31-58E22B739B37@rug.nl">F925B208-9BF1-4C79-AC31-58E22B739B37@rug.nl</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br>
<br>
<br>
try the option -ignh, it will ignore the the hydrogen atoms in your<br>
pdb file and generate the ones necessary to the force field you choose.<br>
<br>
On Dec 15, 2009, at 9:52 AM, ashish pandey wrote:<br>
<br>
> Dear all,<br>
> my self ashish and i am trying to dynamics using gromacs.<br>
> i am new in these field. in the time of running Pdb2gmx to create .gro<br>
> file. i am geting these error.<br>
><br>
> Fatal error:<br>
> Atom HA in residue MET 1 not found in rtp entry with 9 atoms<br>
><br>
> please help me sortout these problem.<br>
><br>
> --<br>
> Ashish Pandey<br>
> NIPER India<br>
> --<br>
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End of gmx-users Digest, Vol 68, Issue 77<br>
*****************************************<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------------------------------------------------------<br>RITURAJ PUROHIT<br>Assistant Professor, Bioinformatics Division<br>
School of Bio-sciences and Technology (SBST)<br>Vellore Institute of Technology, University<br>Address: SBST, VIT University, Vellore-632014,Tamilnadu, India.<br>Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile)<br>Fax; +91-416-2243092, E-mail: <a href="mailto:rituraj@vit.ac.in">rituraj@vit.ac.in</a><br>
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